Biology subjects

Krom, N.

Publications and source records attributed to Krom, N..

5 recordsLinked to original sources

bioRxiv2024

Comparative Transcriptomics of Arabidopsis, Medicago, Brachypodium and Setaria species during Phosphorus limitation

Translating biological knowledge from Arabidopsis to crop species is important to advance agriculture and secure food production in the face of dwindling fertilizer resources, biotic and abiotic stresses. However, it is often not trivial to identify functional homologs (orthologs) of Arabidopsis genes in crops. Combining sequence and expression data can improve the correct prediction of orthologs. Here, we conducted a large-scale RNA sequencing based transcriptomics study of Arabidopsis, Medicago, Brachypodium and Setaria grown side-by-side in Phosphorus (P)-sufficient and P-limited conditions to generate comparable transcriptomics datasets. Comparison of top 200 P-limitation induced genes in Arabidopsis revealed that [~]80% of these genes have identifiable close homologs in the other three species but only [~]50% retain their P-limitation response in the legume and grasses. Most of the hallmark genes of the P-starvation response were found conserved in all four species. This study reveals many known, novel, unannotated, conserved and species-specific regulations of the transcriptional P-starvation response. Identification and experimental verification of expressologs by independent RT-qPCR for P-limitation marker genes in Prunus showed the usefulness of comparative transcriptomics in pinpointing the functional orthologs in diverse crop species. This study provides an unprecedented resource for functional genomics and translational research to create P-efficient crops. HIGHLIGHTComparative transcriptomics reveals novel, known, conserved and specific transcriptome responding to Phosphorus limitation in Arabidopsis, Medicago, Brachypodium and Setaria to facilitate translational research in crops.

molecular biology↗

bioRxiv2024

Integrated GWAS and Transcriptomic Analysis Identify New Candidate Genes for Seminal Root Growth Angle in Wheat (Triticum aestivum L.)

Increased interest in root system architecture (RSA) and its major importance for nutrient and water uptake have intensified the efforts for a detailed study of the different root types within the homorhizic root system found in most monocotyledons as wheat. Mature homorhizic root system comprises two root types regarding their origin: embryonic and pot embryonic. However, knowledge of the different root type ss physiology and RSA plasticity is still limited. In wheat, embryonic roots are the first to develop after seed germination and have an important role in crop establishment. Wheat seedlings develop between 3 and 5 embryonic roots that have the same origin, but they differ in their spatial distribution. The first emerging root of a wheat seedling develops from the base of the embryo and grows vertically down. The rest of the seminal roots emerge from the lateral sides of the embryo and grow with a very specific set-point angle dependent on variety. In this study, we showed that seminal roots with different set-point angle displayed differences in response to gravity and in auxin transport. We hypothesized that the differences in RSA among root types will be directed by differences in their transcriptomic profiles. To that end, we performed an RNA sequencing analysis on both root types. With the aim of gaining a more complete understanding of the seminal root architecture plasticity, we also studied the genetic variability associated with root set-point angle performing a Genome-Wide Association Study in a wheat genetic panel of 200 accessions. Our results combined, uncovered a cluster of genes located in Chromosome 2B that comprises new players in wheat RSA with potential roles in plant response to abiotic stress.

plant biology↗

bioRxiv2022

Elucidating the unknown transcriptional responses and PHR1 mediated biotic and abiotic stress tolerance during phosphorus-limitation

Phosphorus (P) limitation in the majority of world soils is a major constraint for plant growth and crop productivity. RNA sequencing was used to discover novel P-responsive gene transcripts (PRGT) in leaves and roots of Arabidopsis. Hisat StringTie and Cufflinks TopHat transcript assembler were used to analyze reads and identify 1,074 PRGTs with a >5-fold altered abundance during P-limitation. Interestingly, 60% of these transcripts were not previously reported. Among the novel PRGT, 106 were from unannotated genes, and some were among the most P-responsive, including At2g36727 which encodes a novel microRNA. Annotated novel PRGTs encode for transcription factors, microRNAs, small signaling peptides, long non-coding RNAs, defense-related proteins, and transporters, along with proteins involved in many biological processes. We identified several genes that undergo alternative splicing during P-limitation, including a novel miR399 resistant splice variant of PHOSPHATE2 (PHO2.2). Several novel P-responsive genes were regulated by PHOSPHATE STARVATION RESPONSE1 (PHR1), PHR1-LIKE 1 (PHL1) and PHO2. We discovered that P-limited plants show increased resistance to pathogens and drought stress mediated by PHR1-PHL1. Identification of novel P-responsive transcripts and the discovery of the influence of P-limitation on biotic and abiotic stress adds a significant component to our understanding of plant P-signaling. HighlightPhosphorus limitation elicits the expression of several novel genes including many previously unannotated genes, noncoding RNAs, small peptides and alternatively spliced RNAs, and leads to enhanced disease and drought tolerance.

plant biology↗

bioRxiv2021

Application of synthetic peptide CEP1 increases nutrient uptake rates along plant roots

The root system of a plant provides vital functions including resource uptake, storage, and anchorage in soil. Uptake from the soil of macro-nutrients like nitrogen (N), phosphorus (P), potassium (K), and sulphur (S) is critical for plant growth and development. Small signaling peptide (SSP) hormones are best known as potent regulators of plant growth and development with a few also known to have specialized roles in macronutrient utilization. Here we describe a high-throughput screen of SSP effects on root uptake of multiple nutrients. The SSP, MtCEP1 enhanced nitrate uptake rate per unit root length in Medicago truncatula plants deprived of N. MtCEP1 and AtCEP1 enhanced uptake not only of nitrate, but also phosphate and sulfate in both Medicago and Arabidopsis. Transcriptome analysis of Medicago roots treated with different MtCEP1 encoded peptide domains revealed that hundreds of genes respond to these peptides, including several nitrate transporters and a sulfate transporter that may mediate the uptake of these macronutrients downstream of CEP1 signaling. Likewise, several putative signaling pathway genes were induced in roots by CEP1 treatment. Thus, a scalable method has been developed for screening synthetic peptides of potential use in agriculture, with CEP1 shown to be one such peptide.

plant biology↗

bioRxiv2019

Chromosome-level genome reference of Venturia effusa, causative agent of pecan scab

Pecan scab, caused by Venturia effusa, is a devastating disease of pecan (Carya illinoinensis), which results in economic losses on susceptible cultivars throughout the southeastern U.S. To enhance our understanding of pathogenicity in V. effusa, we have generated a complete telomere-to-telomere genome reference of V. effusa isolate FRT5LL7-Albino. By combining Illumina MiSeq and Oxford Nanopore MinION data, we assembled a 45.2 Mb genome represented by 20 chromosomes and containing 10,820 genes, of which 7,619 have at least one functional annotation. The likely causative mutation of the albino phenotype was identified as a single base insertion and a resulting frameshift in the gene encoding the polyketide synthase ALM1. This genome represents the first full chromosome level assembly of any Venturia species.

genomics↗